The invention relates to a high-iron, high-manganese and high-ammonia nitrogen underground water integral treatment apparatus and a method thereof, and belongs to the field of water supply purification. The problem of unable effective synergistic removal of iron, manganese and ammonia nitrogen of high-ammonia nitrogen underground water treatment, and the problems of low iron and manganese removal rate, long treatment process, long running cycle, complex running management and large investment due to unstable manganese removal when the ammonia nitrogen content is high are solved in the invention. The apparatus is composed of an underground water aeration tank, an integral two-stage filtration pot, an inlet water submersible pump, a filtration pot water inlet pipe, a filtration pot water outlet pipe, a backwashing pipe, a backwashing pump and a clear water tank. The method comprises the following steps: 1, starting a filter column; 2, culturing the filter column; and 3, carrying out an underground water treatment stage to complete efficient and stable purifying treatment of the high-iron, high-manganese and high-ammonia nitrogen underground water. The apparatus and the method have the advantages of simple process flow, small occupied area, strong impact resistance, low running cost, and high water yield; and the apparatus and the method allow the iron content, the manganese content and the ammonia nitrogen content of outlet water to be respectively reduced to 0.1mg / L, 0.05mg / L and 0.1mg / L or below.